The versatile attacker is no longer an undisputed starter under Pep Guardiola and is believed to be unhappy with his lack of regular game time at the Allianz Arena.
Manchester United are supposedly closely monitoring the 24-year-old's situation in Bavaria and Rummenigge is ready to sit down with Muller to discuss the player's future.
"If a player does not feel well at Bayern Munich, he should come to my office," the FCB chief was quoted as saying by Bild.
"We will have to talk about things like that."
Muller has a contract with Bayern until the summer of 2017. He has netted 13 goals in 30 Bundesliga appearances this term.